You only need to post on stack overflow or here, there's a feed that shows up the questions (so this is showing up twice).
To copy and paste my answer from stack overflow:
I've done this trick but only in portal, i can only guess if the same thing done in portal+aspx.net doesn't work, that the coding difference in one rendering all the zones and the other only loading webparts into the existing zones may be the issue.
Out of curiosity, why are you doing aspx.net+portal? There is very little you can't do in pure Portal (plus a custom control) than you can do in aspx.net+portal, plus it's super annoying to have a hard coded master template. I would convert.